Enter text search terms in the search field then press the Search Button
to progress to the next tab.

Text can consist of one or more words, either on one or more lines.
The search text can also include tabs. All tabs and new line characters that
are entered will be converted to spaces. This allows the copying and pasting
of text from various applications.

Text Search Options

Use the Text Search Options to help refine how the search behaves.

Auto Complete

Auto-complete is based upon all the words within Gataca that appear in the
name, description, and definition from all concepts. When the drop-down list appears,
use the arrow keys or mouse to to make a selection, then use TAB or ENTER to apply
it. To cancel an auto-complete selection, press ESC, and then the TAB and ENTER
keys will behave normally.

Session History Tab

The last 10 Text Search Queries are stored and are accessible under
the Session History tab.

Examples Tab

For examples on how to use boolean logic, grouping, proximity searches,
or even fuzzy searches please click on the Examples tab.

Gataca is supported by...

Filtering Search Results (Facets)

Text Search Query:

Text Search Options:

none

Guided Help
Showing
of

Filter Results - Basics 1 - Major Organization of Filters

These filter results are grouped first by category with the default being
All Categories.

Within each category's filter set, there exists multiple
filter groups that have a list of filter topics. The filter topics
are based upon the search terms that have been entered on the
Text Search tab and the number
in parenthesis represents an approximate concept count that share the same value.

Clicking on the concept count will apply that filter and take you to the next tab,
the Search Results. Otherwise
after selecting filters, click on the Next button to go to the
Search Results
tab to see the results of the text terms with the applied filters.

For more information about filtering, please see the side bar below titled Notes On
Filters or Help topics of
Filters
and
Filters - Try it!
.

Filter Results - Categories and Boolean Relationships

Click the Next button to view the Text Search Results.

Gataca contains data from many data sources of which similar data is group together
in to Categories. Each category may have data elements that are not
found in other categories and they may also share similar types of data. Any data
element (field, column, data type, etc...) that has a fairly small set of unique
values (generally no more than 30) for the whole category can be used as a filter
(facet) to help zero in on interesting data.

Each category has its own set of filters that can be set under the pane
Category Being Filtered. The category of ALL is a general set of
filter groups that apply to all categories. If there are any filters enabled for a
given category then their count will be shown after the category name.

Filters are listed by topics and these topics comprise a filter group. Each
group contains a set of one or more filters.

Boolean Relationships

The set of selected filters within each group forms an OR
relationship between
each other when more than one item is checked.

The relationship between groups that have selected items will behave as
an AND relationship in the query results.

An example where letters represent groups and numbers
represent items within the group.

(A1 OR A3 OR A4 OR A12) AND (C3 OR C7 OR C30)

This illustrates a selection from Groups
A and C with nothing selected from B such that B's filters will
NOT constrain the output.

Selecting Filters

When no items are checked within one group, then that group will not be used
as a filter, which will have an effect as if all items were checked. BUT...

Selecting all items in a group that has more than
30 items IS NOT the same as selecting NO items in the group;
any concept that is associated with with the 31st or greater item will NOT
be included in the Search Results tab.

By default, only the first 15 items are displayed in the group, sorted by the
number of concepts associated with that item. Additional items can be displayed
by clicking on the
icon
at the bottom of the group. A maximum of 30 items will be
displayed. If there are more than 30 items in a group, they cannot be displayed;
try applying filters in another group or the ALL category to reduce the
number of items in any group
that has more than 30 items.

Example of selecting other facet item to reduce a group's items: Perform a text search on
the gene apob and click Next to get to the
Filter Results tab. Notice under Semantic Type there are about 16
items listed. Check the Disease category and then click on the All Categories
under the pane Category Being Filtered to apply and update the selections.
Notice how the Semantic Type group has been reduced down to 9 items.

The result of applying the filters will impact the number of concepts that are
presented on the Search Results tab. If item A3 had a count of 100 and
item C7 had a count of 50, these total counts of how many concepts are returned
depends upon the number of concepts that have a representation in both A3ANDC7. There does exist a probability that there are
NO concepts that have both, and when such a condition occurs the
results will be empty. There are also many concepts that have more than one possible
filter for any given filter group. An example with the Semantic Type group is that
some concepts may be associated with more than one semantic type.

To see how the selection of various filters will impact
the Text Search Results, just click on the currently selected category in the
Category Being Filtered pane which will refresh the facets and their
estimated totals.

Limitations and Gotchas

There does exist some filter groups where the total number of concepts that are represented
in that group is far less than the number of concepts that would be returned by the search
if no filter items in the group are selected. This is normal and due to the wide range of
data that is included in Gataca. For example: A search on "APOB" will result in about 9
concepts in the Gene category, but only 7 have entries for their respective
Chromosome
filter. This difference is due to multiple data sources contributing to the Gene category
and at least one of those sources do not identify this information.

If a Category Being Filtered does not list any groups, it may be attributed
to no results based upon the search term, or filter(s) set at the ALL
category level is blocking any results for another category. An example would be a
search on "APOB" and then at the ALL category level setting a Group
filter on Disease. Then when you click on the Anatomy category under the
Category Being Filtered pane you will see no results. This is due to
the setting of filters only for diseases and hence any other categories, such as anatomy,
will have no concepts associated with them.

Remember the filter groups and filter items that
are displayed represents the actual search results with all prior filters applied.

Results Filtering

Category - All Categories

Listing of all Applied Filters

No Filters are in Effect

none

Category Being Filtered

Clicking any category below, including the current category, will apply and refresh all filters.

All Categories

Disease

Anatomy

Gene

Jax Mouse Phenotype

Human Phenotype

Gene Ontology: Biological Processes

Gene Ontology: Cellular Component

Gene Ontology: Molecular Function

Pathway

Drug

Genomic Expression Atlas -- Microarray Datasets

PubMed

CoExpression Atlas

CoExpression

Interactions

Text Search Results

Text Search Query:

none

Text Search Options:

none

Guided Help
Showing
of

Search Results Basics

The text search results are now displayed in the appropriate category panes.
If a category does not include any search results, it will will automatically be
collapsed.

If a filter has been applied to a given category, then the filter values will be
displayed right-below the category header.

Filters can be dynamically removed
from the Search Results tab without having to return to the
Filter Results tab by clicking on the super-scriptx that is to the right of each listed filter or even their filter
group. When a filter or filter group is removed, the category will be dynamically
updated to reflect the elimination of those constraints. This can be a valuable tool
to help quickly expand a query that may be too constrained.

To add more filters, click on the Back Button at any time and
adjust any of the filters.

Something 2

Use the Text Search Options to help refine how the search behaves.

Text Search Results

All

Disease: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Anatomy: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Gene: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Jax Mouse Phenotype: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Human Phenotype: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Gene Ontology: Biological Processes: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Gene Ontology: Cellular Component: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Gene Ontology: Molecular Function: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Pathway: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Drug: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Genomic Expression Atlas -- Microarray Datasets: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

PubMed: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

CoExpression Atlas: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

CoExpression: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Interactions: 0

No results.

Concepts (w/Genes): 0
(0)
Selected (w/genes): 0
(0)

Details

Terms of Use

Hide Disclaimer

Notice and Disclaimer: This computer software is developed at Division of Biomedical
Informatics, Cincinnati Children's Hospital Medical Center (BMI CCHMC), Cincinnati,
OH 45229. All rights in the computer software are reserved by Division
of Biomedical Informatics, Cincinnati Children's Hospital Medical
Center, Cincinnati, OH 45229 We do not make any warranty, express, or
imply, or assume any liability for the use of this software.

Do not use results from GATACA to make clinical decisions.

GATACA may link to third-party sites and use third-party data.
Use of third-party sites and/or third-party data may
subject the user to a third-party's terms of use and
may require a third-party licensing
agreement.

GATACA and BMI CCHMC, do not guarantee, approve or endorse the information,
data or products available at these sites or their data.
Use of this
website is taken as an agreement to these terms of usage.

Data

Data - ToppGene Sources

The vast majority of all data in Gataca is from ToppGene so its credits cover data sources that are used
within Gataca. The primary reason for utilizing the same sources between these applications is to help
ensure consistancy between them. ToppGene, and Gataca, uses data from over 20 sources.

Data - GUDMAP

Data - UMLSKS

Software

Software - Solr

Software - PrototypeJS

Prototype JavaScript framework, version 1.7
(c) 2005-2010 Sam Stephenson
Prototype is freely distributable under the terms of an MIT-style license.
For details, see the Prototype web site: http://www.prototypejs.org/

Software - script.aculo.us

NOTE: Only the effects.js and dragdrop.js modules from Script.aculo.us are
being used.

// script.aculo.us scriptaculous.js v1.9.0, Thu Dec 23 16:54:48 -0500 2010
// Copyright (c) 2005-2010 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
//
// Permission is hereby granted, free of charge, to any person obtaining
// a copy of this software and associated documentation files (the
// "Software"), to deal in the Software without restriction, including
// without limitation the rights to use, copy, modify, merge, publish,
// distribute, sublicense, and/or sell copies of the Software, and to
// permit persons to whom the Software is furnished to do so, subject to
// the following conditions:
//
// The above copyright notice and this permission notice shall be
// included in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
// LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
// OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
//
// For details, see the script.aculo.us web site: http://script.aculo.us/

Software - Oracle Enterprise Edition

Software - Modernizr

modernizr provides simple interfacing to check to see what features are available within the client's browser.
This is predomantly used to test for HTML 5 features such as canvas or local storage support.

Software - JQTouch

Software - jQuery

Software - tablesort

Copyright (c) 2006 Andrew Tetlaw
http://tetlaw.id.au/view/blog/table-sorting-with-prototype/
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.